From b3e9398c3affa964fdc8cf090eb5c149f7a6bf47 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Fri, 4 Mar 2016 20:47:57 +0100 Subject: [PATCH 1/4] Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship --- .../tool_dependencies/recipe/tag_handler.py | 42 +++---------------- 1 file changed, 6 insertions(+), 36 deletions(-) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py index f18588e152b..eeb69f9dd01 100644 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -360,34 +360,6 @@ class Repository( RecipeTag, SyncDatabase ): env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) return env_sh_file_path - def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( self, tool_shed_url, name, owner, changeset_revision ): - sa_session = self.app.install_model.context - # The protocol is not stored, but the port is if it exists. - tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url ) - tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \ - .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, - self.app.install_model.ToolShedRepository.table.c.name == name, - self.app.install_model.ToolShedRepository.table.c.owner == owner, - self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ - .first() - if tool_shed_repository: - return tool_shed_repository - # The tool_shed_repository must have been updated to a newer changeset revision than the one defined in the repository_dependencies.xml file, - # so call the tool shed to get all appropriate newer changeset revisions. - text = suc.get_updated_changeset_revisions_from_tool_shed( self.app, tool_shed_url, name, owner, changeset_revision ) - if text: - changeset_revisions = listify( text ) - for changeset_revision in changeset_revisions: - tool_shed_repository = sa_session.query( self.app.install_model.ToolShedRepository ) \ - .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, - self.app.install_model.ToolShedRepository.table.c.name == name, - self.app.install_model.ToolShedRepository.table.c.owner == owner, - self.app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ - .first() - if tool_shed_repository: - return tool_shed_repository - return None - def handle_complex_repository_dependency_for_package( self, elem, package_name, package_version, tool_shed_repository, from_tool_migration_manager=False ): """ @@ -398,17 +370,15 @@ class Repository( RecipeTag, SyncDatabase ): and package_version is being installed. """ handled_tool_dependencies = [] - tool_shed = elem.attrib[ 'toolshed' ] - # The protocol is not stored, but the port is if it exists. - tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed ) + tool_shed_url = elem.attrib[ 'toolshed' ] required_repository_name = elem.attrib[ 'name' ] required_repository_owner = elem.attrib[ 'owner' ] default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ] - required_repository = \ - self.get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( tool_shed, - required_repository_name, - required_repository_owner, - default_required_repository_changeset_revision ) + required_repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed_url, + required_repository_name, + required_repository_owner, + default_required_repository_changeset_revision ) + tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url ) tmp_filename = None if required_repository: required_repository_changeset_revision = required_repository.installed_changeset_revision From d6e38c7d482eae65fc135cd65a13b7f215220cd5 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Fri, 4 Mar 2016 21:17:05 +0100 Subject: [PATCH 2/4] remove unused import --- .../galaxy_install/tool_dependencies/recipe/tag_handler.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py index eeb69f9dd01..2198ceb8512 100644 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -2,8 +2,6 @@ import logging import os import tempfile -from sqlalchemy import and_ - from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY from galaxy.util import listify from tool_shed.util import basic_util From 90fcd8c668865ce109b3fbc011319a9794e9e47f Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Mon, 14 Mar 2016 14:42:07 +0000 Subject: [PATCH 3/4] Handle sections in view workflow Fixes 1723 --- templates/webapps/galaxy/workflow/display.mako | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/templates/webapps/galaxy/workflow/display.mako b/templates/webapps/galaxy/workflow/display.mako index 367b8118f9c..51f27176d4b 100644 --- a/templates/webapps/galaxy/workflow/display.mako +++ b/templates/webapps/galaxy/workflow/display.mako @@ -30,6 +30,15 @@ <% new_prefix = prefix + input.name + "|" %> ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, prefix, step )} ${do_inputs( input.cases[ current_case ].inputs, group_values, new_prefix, step, other_values )} + %elif input.type == "section": + <% new_prefix = prefix + input.name + "|" %> + <% group_values = values[input.name] %> +
${input.title}:
+
+
+ ${do_inputs( input.inputs, group_values, new_prefix, step, other_values )} +
+
%else: ${row_for_param( input, values[ input.name ], other_values, prefix, step )} %endif From 18473a187e019421933746abb31f8b226e828b80 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Tue, 15 Mar 2016 19:41:09 +0100 Subject: [PATCH 4/4] Ensure chrom, start, end as bytestring in BamDataProvider --- lib/galaxy/visualization/data_providers/genome.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index a4d0a9a0121..ebe634b3c78 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -888,6 +888,9 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): """ # Fetch and return data. + chrom = str(chrom) + start = int(start) + end = int(end) try: data = data_file.fetch( start=start, end=end, reference=chrom ) except ValueError: